Journal Of Structural Biology[JOURNAL]
Sun
200 papers
Targeting Helicobacter pylori thymidylate kinase: structural insights and validation of novel inhibitors.
Kumari K, Khan FM, Bose M … +4 more , Ls RJ, Yadav A, Mondal N, Gourinath S
J Struct Biol · 2026 Jun · PMID 41935652 · Publisher ↗
Thymidine (deoxythymidine triphosphate) plays very important role in DNA synthesis, replication and repair. Therefore, thymidine synthesis pathway enzymes are crucial for the survival of the organism and hence are potent...
Thymidine (deoxythymidine triphosphate) plays very important role in DNA synthesis, replication and repair. Therefore, thymidine synthesis pathway enzymes are crucial for the survival of the organism and hence are potent therapeutic targets. Thymidylate kinase (TMPK) is at the junction of de novo synthesis pathway and salvage pathway of thymidine synthesis. TMPK is widely recognized as a potential therapeutic target. Inhibiting TMPKs would be an effective technique for discovering medications to treat infectious disorders like bacterial and parasite infections. The slight variation in active sites between human TMPK (hTMPK) and pathogen TMPKs provide support for the development of specific inhibitors. Here, we report the crystal structure of thymidylate kinase from Helicobacter pylori (HpTMPK) at 2.5 Å. The three-dimensional structure of HpTMPK depicts two conserved regions DRX motif and P loop. The highly flexible LID region was absent in HpTMPK crystal structure. Chemdiv library was screened against HpTMPK and the compounds were shortlisted based on the docking scores. Our in-vitro enzyme inhibition study shows that compound F725_0025 exhibits the best inhibition with an IC of 84 µM and a strong affinity of 10.7 µM. It inhibits Helicobacter pylori (H. pylori) with an IC value of 30.14 µM. According to the growth curve of H. Pylori in the presence of inhibitory chemicals, F725_0025 may be a promising lead therapeutic molecule to combat H. pylori infection.
Investigating oncolytic virus M1-Associated vesicles using 3D electron microscopy.
Nie L, Li Y, Song D … +4 more , Chen D, Yan G, Lin Y, Zhang Q
J Struct Biol · 2026 Jun · PMID 41903911 · Publisher ↗
The oncolytic virus M1 (OVM) is recognized as an effective and promising oncolytic virus. Extensive research has been conducted to elucidate the molecular mechanisms underlying OVM's selective targeting and destruction o...
The oncolytic virus M1 (OVM) is recognized as an effective and promising oncolytic virus. Extensive research has been conducted to elucidate the molecular mechanisms underlying OVM's selective targeting and destruction of cancer cells. However, a comprehensive understanding of the biological processes involved in viral assembly and maturation within cancer cells remains elusive. In this study, we employed volume three-dimensional electron microscopy to examine Hs578T cells infected with OVM. Our findings not only identified four distinct types of cytopathic vesicles (CPVs) that emerged within the infected cancer cells but also revealed that CPV-II comprises two maturation-stage subtypes, CPV-II-1 and CPV-II-2, with the latter forming tree-like intracellular tunnel networks. Furthermore, the data presented here provide evidence for the release of mature virions through cytopathic vesicles type III. Collectively, our research sheds light on the developmental process of virus-associated vesicles, updates our understanding of OVM's viral release mechanisms, and refines the characterization of the OVM life cycle in cancer cells.
Binding of the elastin peptide VGVAPG and lactose to the human elastin binding protein.
Haslak ZP, Belloy N, Debelle L … +2 more , Dauchez M, Baud S
J Struct Biol · 2026 Jun · PMID 41895457 · Publisher ↗
Elastin-derived peptides (EDPs) interact with elastin-binding protein (EBP), a key component of the elastin receptor complex, modulating cellular processes such as protease activation, apoptosis, and chemotaxis via regul...
Elastin-derived peptides (EDPs) interact with elastin-binding protein (EBP), a key component of the elastin receptor complex, modulating cellular processes such as protease activation, apoptosis, and chemotaxis via regulation of NEU-1 sialidase activity. Despite their therapeutic relevance, the structural basis of EDP-EBP interactions remains poorly understood. Here, we present the first full-length homology model of EBP (residues 29-516), constructed and validated through duplicate 1 microsecond long molecular dynamics (MD) simulations. Molecular docking of VGVAPG (as a representative EDP) and lactose (as a representative galactosugar) followed by MD simulations, allowed us to identify key binding residues: D98, E99, S104, and S136 for VGVAPG; and E99, S101, S104, N116, Q124, E137, and Y139 for lactose. These data reveal a shared binding region within residues 83-139, suggesting a competitive binding between EDPs and galactosugars. Furthermore, EBP residues P233 and I234 were implicated in potential interactions with PPCA or NEU-1, contributing to ERC assembly. These findings offer new insights into the molecular recognition mechanisms of EBP and provide a foundation for the design of EBP-targeted elastin peptide antagonists.
Discovery and computational characterization of a novel cryptic pocket in human farnesyl pyrophosphate synthase.
Pandya V, Wilson KA, Leung CY … +2 more , Tsantrizos YS, Park J
J Struct Biol · 2026 Jun · PMID 41865847 · Publisher ↗
The mevalonate pathway provides isoprenoid building blocks required for the biosynthesis of more complex downstream products, including cholesterol, as well as for the posttranslational prenylation of membrane-associated...
The mevalonate pathway provides isoprenoid building blocks required for the biosynthesis of more complex downstream products, including cholesterol, as well as for the posttranslational prenylation of membrane-associated proteins. Farnesyl pyrophosphate synthase (FPPS) is a key regulatory enzyme in this pathway and an established drug target for bone-resorption disorders, with more recent interest in its inhibition as a potential anticancer strategy. In addition to classical active-site inhibitors such as nitrogen-containing bisphosphonates, several chemically distinct small molecules inhibit FPPS via an allosteric site involved in a product-mediated feedback regulation. Here, we report the discovery of a previously unrecognized ligand-binding site in FPPS. Crystallographic analysis reveals that several bisphosphonate compounds, previously thought to bind to the allosteric site under metal-free conditions, instead bind to a distinct cryptic pocket. Located adjacent to the known allosteric site, this pocket is absent in the native enzyme conformation. Its formation is driven by a conformational rearrangement of the C-terminal helix, which alternates between opening the allosteric pocket and the cryptic pocket in a mutually exclusive manner. Molecular dynamics simulations indicate that the cryptic pocket does not open spontaneously from the native state on the simulated timescale and likely requires ligand binding. Once induced, the open conformation is stabilized by residues Phe239 and Ile348. Together, these findings expand the known conformational landscape of FPPS and identify a new ligandable site that may be relevant for future chemical biology and drug discovery efforts.
Molecular dynamics simulations refine the pathogenicity of ACVRL1 kinase domain variants by quantifying impacts on ATP binding in pulmonary arterial hypertension.
Borovikova I, Uporov I, Okhrimenko G … +4 more , Zamyatin V, Dankovtseva E, Zateyshchikov D, Poptsova M
J Struct Biol · 2026 Jun · PMID 41839337 · Publisher ↗
Single amino acid substitutions in the ATP-binding domain of ACVRL1, a key receptor in the bone morphogenetic protein (BMP) signaling pathway, are frequently classified as variants of uncertain significance (VUS), compli...
Single amino acid substitutions in the ATP-binding domain of ACVRL1, a key receptor in the bone morphogenetic protein (BMP) signaling pathway, are frequently classified as variants of uncertain significance (VUS), complicating molecular diagnosis for pulmonary arterial hypertension (PAH) and Hereditary Hemorrhagic Telangiectasia (HHT). Since aberrant ATP binding disrupts downstream SMAD1/5/8 phosphorylation, we employed molecular dynamics (MD) simulations to quantitatively assess the functional impact of these variants. We first validated our approach on 20 known pathogenic/likely pathogenic variants within 5Å of the ATP-binding site, finding that 18 (90%) caused significant alterations in binding affinity (|d| ≥ 0.8, p < 0.001). We then applied this protocol to all known VUS, conflicting, and unclassified variants within the same region, reclassifying 20 of 32 (63%) as likely pathogenic. Comprehensive in silico mutagenesis of all possible substitutions at ATP-binding pocket positions, combined with InterVar classification under HHT phenotype, enabled reclassification of 9 of 12 (75%) VUS as likely pathogenic. Finally, we demonstrated the applicability of this approach in two PAH patients with HHT carrying ACVRL1 VUS. This work establishes MD simulation of ATP-binding affinity as an effective and scalable tool for the functional interpretation of kinase variants, with broad potential for application across other disease-associated kinases.
An inactive Zika NS2B-NS3pro protease construct for investigating allosteric inhibitors.
Ngo KH, Lattmann S, Anindita PD … +4 more , Liew CW, Harris RS, Luo D, Kang C
J Struct Biol · 2026 Jun · PMID 41833763 · Publisher ↗
The Zika virus protease, composed of the cofactor region from NS2B and the N-terminal region of NS3, plays a critical role in viral polyprotein maturation and represents an attractive therapeutic target. However, develop...
The Zika virus protease, composed of the cofactor region from NS2B and the N-terminal region of NS3, plays a critical role in viral polyprotein maturation and represents an attractive therapeutic target. However, developing small-molecule inhibitors for its highly hydrophilic active site remains challenging, highlighting the importance of pursuing allosteric inhibition strategies. In this study, we engineered an NS2B-NS3 protease containing an 18-residue NS2B sequence linked to the N-terminal region of NS3 via a glycine-rich linker. We determined its crystal structure and obtained the solution NMR spectrum with backbone resonance assigned. This new construct was used in fragment screening and two new fragments were identified. This design excludes the C-terminal part of NS2B cofactor region, whose conformation is influenced by substrate or inhibitor binding, making the construct particularly valuable for screening and characterizing allosteric inhibitors.
Effects of mineral nutrition on the cuticle structure of Armadillidium vulgare.
Tatsunami S, Okada S, Yamaguchi K … +1 more , Kyono A
J Struct Biol · 2026 Jun · PMID 41819392 · Publisher ↗
The terrestrial isopod Armadillidium vulgare possesses a hierarchically organized tergite cuticle mineralized with calcium carbonate, comprising crystalline calcite and amorphous calcium carbonate (ACC). In this study, w...
The terrestrial isopod Armadillidium vulgare possesses a hierarchically organized tergite cuticle mineralized with calcium carbonate, comprising crystalline calcite and amorphous calcium carbonate (ACC). In this study, we assessed the effects of dietary calcium carbonate polymorphs (calcite, aragonite) and a non-carbonate control (quartz) on cuticle mineralization and layer-specific microstructural organization. Isopods were reared under controlled-feeding conditions using calcite, aragonite, or quartz, and their cuticles were analyzed using scanning electron microscopy (SEM), Raman spectroscopy, and synchrotron X-ray diffraction (XRD). SEM observations indicated that diets containing calcite or aragonite promoted marked thickening and development of mineralized lamellar structures within the exo- and endocuticles, whereas quartz-fed individuals exhibited significantly reduced cuticle mineralization. Raman spectroscopy revealed that the endocuticle consistently contained calcite-type ACC, irrespective of whether calcite or aragonite was provided as the dietary carbonate source. In contrast, the exocuticle exhibited unique characteristics of a more structurally ordered carbonate phase, consistent with a transitional state between ACC and crystalline calcite. Synchrotron XRD analyses of bulk cuticle specimens detected only calcite reflections across all feeding conditions, with no evidence of aragonite even in aragonite-fed isopods, indicating a selective crystallization process. These findings demonstrate that A. vulgare establishes a predominantly calcite-based carbonate system within its cuticle-comprising calcite and calcite-type ACC-largely independent of the external calcium carbonate polymorph source. Polymorph-independent ACC stabilization, layer-dependent carbonate ordering, and exclusive calcite crystallization provide insights into biomineralization mechanisms in terrestrial isopods and establish a framework for future research on carbonate phase evolution in cuticle architecture and function.
3DDF-VAE: Dual-frequency variational autoencoder with pose-consistency validation for rare cryo-EM conformation discovery.
Chen Y, Li F, Dong H … +4 more , Wang X, Zhang F, Hu B, Wan X
J Struct Biol · 2026 Jun · PMID 41819391 · Publisher ↗
Revealing the 3D conformational variability of biomolecules is crucial for understanding their function, while cryo-EM reconstruction of rare states remains difficult due to data imbalance and structural detail loss in e...
Revealing the 3D conformational variability of biomolecules is crucial for understanding their function, while cryo-EM reconstruction of rare states remains difficult due to data imbalance and structural detail loss in existing generative models. We present a dual-stage pipeline consisting of a generative stage and a validation stage. In the generative stage, we employ a 3D dual-frequency variational autoencoder (3DDF-VAE) that separately models low- and high-frequency components of protein density maps to enhance global coherence and local structural detail. In the validation stage, a pose-consistency projection strategy evaluates the generated maps by comparison with the original 2D particles. Experiments on integrin αVβ8, T50S ribosome, and SARS-CoV-2 spike datasets demonstrate that our method produces high-quality density maps, identifies rare conformations, and reconstructs plausible intermediates, while ablation studies confirm the benefits of frequency separation and parameter optimization. This integrated generative-validation framework improves resolution, enhances rare conformation detection, and offers a data-driven approach to explore conformational heterogeneity in complex biomolecular systems.
Leveraging deep learning semantic segmentation for imaging coral skeletons.
Coronel-Zegarra A, Knaub JL, Merk V … +1 more , Pandya A
J Struct Biol · 2026 Jun · PMID 41819390 · Publisher ↗
Micro-computed tomography and semantic segmentation provide insights into the structural hierarchy of biomineralized tissues, as exemplified by stony coral skeletons. Non-destructive imaging reveals mechanistic aspects o...
Micro-computed tomography and semantic segmentation provide insights into the structural hierarchy of biomineralized tissues, as exemplified by stony coral skeletons. Non-destructive imaging reveals mechanistic aspects of skeletal growth, including variations in porosity, density, and skeletal thickness across species and in the context of disease. Recent developments in semantic segmentation based on convolutional neural network models are poised to transform the streamlined analysis of large 3D tomography datasets, surpassing the performance of traditional segmentation methods. In this work, a series of U-Net deep learning models were trained and applied on exemplary micro-CT datasets from stony corals pertaining to Montastraea cavernosa and Porites astreoides species for the segmentation of pores and skeleton. The models were statistically evaluated, revealing that Attention U-Net was the top performer with respect to computational efficiency, accuracy, and generalizability, followed by U-Net++ and standard U-Net. Our analysis highlights accuracy limitations of U-Net-based deep learning segmentations that can result in false-positive or false-negative classifications. The segmented 3D models were utilized to perform porosity, bulk density, and thickness analyses of each dataset, revealing quantitative differences between the two species, as well as between healthy and stony coral tissue loss disease afflicted M. cavernosa coral skeletons. This work provides a framework for streamlined training and deployment of deep learning models for semantic segmentation of calcified tissues that inform our understanding of skeletogenesis and growth patterns across species and pathogenesis contexts.
Comparative performance of structural aligners in functional domain annotation.
Borujeni PM, Salavati R
J Struct Biol · 2026 Jun · PMID 41786230 · Publisher ↗
Accurate protein domain annotation is essential for inferring protein function, and databases such as Pfam provide sequence-derived signatures for thousands of domain families. Because protein structure is more evolution...
Accurate protein domain annotation is essential for inferring protein function, and databases such as Pfam provide sequence-derived signatures for thousands of domain families. Because protein structure is more evolutionarily conserved than sequence, structure-based searches can detect homologous relationships even at low sequence identity (typically below 30%), where pairwise sequence aligners often lose sensitivity. Here, we leverage AlphaFold-derived structures of Pfam domain instances to systematically evaluate structure-based versus sequence-based methods for Pfam annotation. We benchmarked three structural aligners (Reseek, Foldseek, TM-align) against sequence-based methods (MMseqs, HMMER) using both exhaustive all-against-all searches and a split-family design that enables direct comparison of pairwise and profile-based ranking performance. We also evaluated residue-level alignment accuracy using Pfam multiple sequence alignments as reference and investigated whether profile-derived information can improve structural hit ranking. In all-against-all searches, Reseek achieved the highest sensitivity up to the first false positive (AUC = 0.85), outperforming Foldseek (0.81), TM-align (0.76), and MMseqs (0.46). In split-family evaluation, HMMER remained superior (maximum F1 = 0.991), highlighting the continued strength of sequence-profile approaches for family-level annotation. Performance varied substantially across domain families, with average sequence identity emerging as the strongest predictor of success. Structural aligners consistently produced more accurate residue-level mappings than pairwise sequence methods. Finally, incorporating profile-derived information via rescoring improved structural annotation performance for short domains, suggesting a path toward profile-informed structure-based domain annotation.
Linking protein aggregation and structural stability to predict pathogenic MYH7 variants via machine learning.
Pyankov IA, Kokorina MA, Rychkov GN … +3 more , Kostareva AA, Uspenskaya MV, Kajava AV
J Struct Biol · 2026 Jun · PMID 41780808 · Publisher ↗
As genome and gene sequencing rapidly expand, data increasingly outpace studies linking genetic variants to specific diseases, making computational methods for associating potential mutations with pathology both essentia...
As genome and gene sequencing rapidly expand, data increasingly outpace studies linking genetic variants to specific diseases, making computational methods for associating potential mutations with pathology both essential and feasible. We found that disease-causing variants associated with Myosin Storage Myopathy (MSM) generally destabilize the MYH7 α-helical coiled-coil domain more than non-disease-associated variants, and structural mapping revealed that pathogenic variants cluster in locally unwound regions of the coiled-coil dimer, suggesting that changes in these strained sites may promote dimer destabilization and aggregation. However, these features alone are insufficient to reliably predict hereditary Myosin Storage Myopathy. By integrating protein aggregation, structural stability, and additional informative features, we developed RDSM-MYH7, a machine learning-based predictor for assessing the pathogenicity of missense mutations in the MYH7 rod domain. RDSM-MYH7 achieved superior performance (F1 = 0.869, accuracy = 0.875), compared to existing tools, and can be applied to individual gene sequencing data to identify pathogenic MYH7-variants associated with storage myopathy. Its implementation in clinical screening could facilitate early diagnosis of myopathies and other hereditary protein storage diseases, in which protein unfolding precedes pathological aggregation.
ProPicker: Promptable segmentation for particle picking in cryogenic electron tomography.
Wiedemann S, Fabian Z, Soltanolkotabi M … +1 more , Heckel R
J Struct Biol · 2026 Jun · PMID 41763621 · Publisher ↗
Cryogenic electron tomography (cryo-ET) produces detailed 3D images (tomograms) of cellular environments. A key step in cryo-ET data analysis is detecting all instances of a specific particle across tomograms, called par...
Cryogenic electron tomography (cryo-ET) produces detailed 3D images (tomograms) of cellular environments. A key step in cryo-ET data analysis is detecting all instances of a specific particle across tomograms, called particle picking. This is a challenging object detection task due to strong noise, artifacts, and the crowded cellular context. Here, we propose ProPicker, a pretrained, promptable 3D segmentation model that enables a flexible and data-efficient particle picking workflow that works well for a broad range of particles. By specifying a prompt, ProPicker is conditioned to detect a particle of interest and can then be used directly or can be fine-tuned to a particle-specific picker for improved accuracy. Experiments on simulated and real-world tomograms show that, using a single prompt, ProPicker achieves performance close to or on par with state-of-the-art methods while being up to an order of magnitude faster. Moreover, ProPicker can detect a range of particles not seen during training. Fine-tuning ProPicker outperforms state-of-the-art particle-specific pickers if limited training data is available.
"QuickStainer": a rapid negative staining device for improved preservation of molecular structure.
Nguyen V, Gautam R, Somavarapu AK … +6 more , Dutta D, Patra A, Ge J, Yengo CM, Padrón R, Craig R
J Struct Biol · 2026 Jun · PMID 41730344 · Full text
Negative staining is a widely used technique for observing macromolecules and their assemblies by transmission electron microscopy. It is commonly employed to optimize specimens for cryo-EM. The stain, typically a uranyl...
Negative staining is a widely used technique for observing macromolecules and their assemblies by transmission electron microscopy. It is commonly employed to optimize specimens for cryo-EM. The stain, typically a uranyl salt, surrounds the structure, providing an outline view at about 20 Å resolution. Many macromolecules are relatively stable and rigid, and negative stain images provide a good representation of their structure. However, some are labile or flexible and their structure or assembly state is altered by binding to the carbon substrate on the grid before specimen staining. In these cases, the negatively stained appearance does not faithfully represent the structure in solution. This problem is reduced when samples are incubated on the carbon surface for short times (5 s) rather than typical times (30-60 s) before staining. To reduce disruption to a minimum, we have developed a rapid negative staining device (QuickStainer) using 3D-printed components, a stepper motor for precisely timed movements, and an Arduino-controlled interface to execute commands. QuickStainer produces consistent sample incubation times as low as 10 ms before staining. Tests show rapid adherence of molecules to the grid and greatly improved structural preservation of labile specimens compared with standard preparation protocols. The design of QuickStainer can accommodate inclusion of additional steps, such as timed incubation with enzyme substrate, before staining.
Corrigendum to "Crystal structure of glyoxysomal citrate synthase 3 from Arabidopsis thaliana reveals a Novel Oligomeric State". [J. Struct. Biol. 218(1) (2026) 108293].
Nishio K, Takagi K, Mizushima T
J Struct Biol · 2026 Mar · PMID 41688312 · Publisher ↗
Abstract loading — click title to view on PubMed.
Structure of the type VI secretion protein VgrS from Salmonella Typhimurium.
Sachar K, Van Schepdael M, Winters KL … +1 more , Prehna G
J Struct Biol · 2026 Mar · PMID 41687690 · Publisher ↗
Enteric bacterial pathogens employ various strategies to colonize the intestine and cause diseases ranging from gastroenteritis to systemic infections. For example, Salmonella enterica utilizes a nanomachine known as the...
Enteric bacterial pathogens employ various strategies to colonize the intestine and cause diseases ranging from gastroenteritis to systemic infections. For example, Salmonella enterica utilizes a nanomachine known as the type VI secretion system (T6SS) to facilitate colonization of the host gut. However, the varied mechanistic details of how the T6SS is loaded with effector proteins remains to be elucidated. Here, we present an X-ray crystal structure of the Salmonella Typhimurium VgrG (VgrS) that serves as platform for T6SS effector loading. Compared to other known structures of VgrG proteins, the VgrS trimer adopts an alternative open conformation within the gp27 region base. The open conformation is due to an extended loop conformation in the gp27 region. This conformation creates a domain extension which docks into the neighboring monomer sequentially around the trimer. Additionally, a comparative structural analysis of VgrS with other VgrG proteins reveals molecular variations that may contribute to specific effector loading mechanisms. Our structural data and molecular analysis highlight the observation that the T6SS of each bacterial species or strain is unique.
GNN2Pfam: Integrating protein sequence and structure with graph neural networks for Pfam domain annotation.
Fenoy E, Bugnon LA, Vitale R … +3 more , Duarte SA, Milone DH, Stegmayer G
J Struct Biol · 2026 Mar · PMID 41633121 · Publisher ↗
The challenge of establishing the relationship between protein sequences and their function cannot yet be considered completely solved. State-of-the-art annotation of Pfam domains is based on hidden Markov models (HMMs)...
The challenge of establishing the relationship between protein sequences and their function cannot yet be considered completely solved. State-of-the-art annotation of Pfam domains is based on hidden Markov models (HMMs) built from hand-crafted sequence alignments. However, while this approach has been highly successful during the last decades since its proposal, there is yet a very large number of proteins that remain unannotated because there is no possible alignment to already known and functionally characterized sequences, or HMM fails to discriminate between similar domains. Adding structural information using deep and graph neural networks (GNNs) presents an opportunity to build upon existing models in those more challenging cases. GNNs excel at capturing complex relationships in data and can learn a model that shares information across all existing families, thus being able to generalize Pfam domain predictions to novel sequences. In this protocol we propose GNN2Pfam, an end-to-end GNN-based method for Pfam family domain annotation. Our strategy allows one single model to be trained for all species and families. This novel proposal uses the protein 3D structure together with a sequence representation obtained from a large pre-trained model. The GNN2Pfam method is based on a graph derived from amino acid interactions in the 3D structure, learning both sequential and structural features from this representation. Experiments show that the proposed GNN-based model can clearly outperform the HMM state-of-the-art predictive performance in Pfam domains annotations. These results suggest that GNN models can be the key component of future protein annotation tools. Data and source code are available at https://github.com/efenoy/GNN2Pfam.
Corrigendum to "High-resolution single particle analysis using a scintillator camera XF416 on CRYOARM300II at 300 kV". [J. Struct. Biol. 218(1) (2026) 108286].
Aramaki S, Tanihara T, Yoshida Y … +3 more , Matsunaga N, Ohdo S, Mayanagi K
J Struct Biol · 2026 Mar · PMID 41605723 · Publisher ↗
Abstract loading — click title to view on PubMed.
Structural features of collagens of warm-blooded and cold-blooded animals that determine differences in their thermal stability.
Meshcheryakova OV, Bogdanov MA, Efimov AV
J Struct Biol · 2026 Mar · PMID 41605373 · Publisher ↗
We have previously shown that the thermal stability of animal collagens correlates with the number of hydrophobic amino acid residues in their composition: the more hydrophobic residues in a molecule, the higher the dena...
We have previously shown that the thermal stability of animal collagens correlates with the number of hydrophobic amino acid residues in their composition: the more hydrophobic residues in a molecule, the higher the denaturation temperature of collagen. In addition, it was found that with the same hydrophobicity, the thermal stability of collagens of cold-blooded animals can be several degrees lower than that of warm-blooded animals. To understand the reasons for this, we studied the amino acid composition and sequences of α1, α2, and α3 chains of type I collagen in warm-blooded and cold-blooded animals. The α3 chain is found only in cold-blooded animals and is represented by sequences for only 6 fish species. The results of the study show that differences in the thermal stability of collagens of warm-blooded and cold-blooded animals may be due to differences in the number of Gly-Gly pairs, Pro, Ala, Met, Ser in collagen subunits. A negative correlation was observed between the number of GGY (Gly-Gly-Yaa, pair Gly-Gly is before Yaa in the sequence) and GGX (pair Gly-Gly is before Xaa in the sequence) and collagen thermal stability. Differences in the amounts of GGY and GGX were also observed between the different types of α1, α2, and α 3 chains. A negative correlation with thermal stability was also observed for Ser. For all chain types, the amount of Pro at position Xaa and Pro at position Yaa was shown to correlate with collagen denaturation temperatures. Moreover, in the α1 and α2 chains of warm-blooded and cold-blooded animals, the positive correlation with Pro(Yaa) was higher than with Pro (Xaa). Similarities were found between the α1 and α3 chains and their differences from the α2 chain in the amount and ratio of Pro (Xaa) and Pro (Yaa).
Crystal structure of glyoxysomal citrate synthase 3 from Arabidopsis thaliana reveals a novel oligomeric state.
Nishio K, Takagi K, Mizushima T
J Struct Biol · 2026 Mar · PMID 41580056 · Publisher ↗
Citrate synthase (CS) is a pivotal enzyme in carbohydrate and energy metabolism, with distinct isoforms present in various eukaryotic compartments, including mitochondria and glyoxysomes in plants. While CSs exhibit dive...
Citrate synthase (CS) is a pivotal enzyme in carbohydrate and energy metabolism, with distinct isoforms present in various eukaryotic compartments, including mitochondria and glyoxysomes in plants. While CSs exhibit diverse oligomeric states, detailed structural information on higher plant non-mitochondrial Type II CSs has been limited. We herein determined the crystal structures of CS 3 from Arabidopsis thaliana (AtCSY3) in complex with oxaloacetate (OAA) and acetyl-coenzyme A (CoA)-OAA at resolutions of 2.0 and 1.7 Å, respectively. These structures revealed that AtCSY3 can form a homo-tetrameric assembly that is distinct from the hexameric Escherichia coli CS and the octameric Ananas comosus CS. The tetrameric arrangement observed in the crystal structure is mediated by hydrogen-bonding and hydrophobic interactions between subunits. Gel filtration chromatography further suggests the presence of a tetrameric species in solution under the purification conditions. Ligand density was observed near the interface between the two dimers in the tetrameric structure; however, no experimental evidence is currently available to determine whether ligand binding affects the oligomeric state or enzymatic activity of AtCSY3. These structures illustrate the structural diversity of CS oligomerization and provide a structural basis for studies of plant glyoxysomal CSs.
Cloneable contrast across all biological length scales.
Borgognoni KM, Guilliams BF, Butz ZJ … +1 more , Ackerson CJ
J Struct Biol · 2026 Mar · PMID 41529762 · Full text
Cloneable contrast in biological microscopy is exemplified by Green Fluorescent Protein (GFP) in fluorescence microscopy. There are no similarly useful cloneable contrast agents that function in biological electron micro...
Cloneable contrast in biological microscopy is exemplified by Green Fluorescent Protein (GFP) in fluorescence microscopy. There are no similarly useful cloneable contrast agents that function in biological electron microscopy. This paper reports a cloneable Selenium NanoParticle (cSeNP) that produces molecular contrast in imaging modalities including cellular electron microscopy, fluorescence microscopy, and X-ray computed tomography. This set of imaging modalities can image all biologically relevant length scales, from subcellular structure to whole organisms. The cSeNP is a ∼5 nm diameter Selenium nanoparticle that is made and conjugated by a protein. Because the cSeNP is electron dense compared to biological molecules, it has high contrast in biological electron microscopy. DNA encoding the cSeNP protein was concatenated to DNA encoding FtsZ, the procaryotic analog of tubulin. FtsZ is membrane associated throughout the cell cycle and localizes to the cleavage furrow of dividing cells. Escherichia coli cells expressing FtsZ-cSeNP fusion proteins were examined by transmission electron tomography and fluorescence light microscopy. These experiments show cSeNP decorated FtsZ filaments and/or cSeNPs in locations that correlate to known FtsZ locations, with less than 5% of cSeNPs in unexpected locations. X-ray imaging shows contrast attributable to cSeNPs is distinguishable from background in E. coli. The cSeNP, therefore, represents a cloneable imaging contrast agent that facilitates location and correlation of proteins-of-interest across all biological length scales. This is especially useful in biological electron microscopy, where larger-area imaging modalities such as fluorescence microscopy are employed to identify sub-areas containing a protein-of-interest to prepare for electron microscopy study.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe